The captain is, without question, the most important member of any given crew. I’ve compiled a list of common mistakes I’ve seen new captains make. I hope you will learn from them (as I have) so that we might make skirmishes more interesting affairs in general.
Before I begin, I will acknowledge that the game mechanics in no way limit the class that a captain may be. You can have a gunner as the captain, with a separate crewman playing pilot and standing at the helm. However, there is no reason I can think of for the captain to not be a pilot. The captain requires information to do his job, and the most information is available at the helm. He can observe much of his own ship from the helm and be able to direct engineers’ efforts to the components most in need of repair, and he usually has the best view for spotting enemy ships. The captain will also have the best knowledge of where the ship should be and how it should be oriented, and as a pilot can make the necessary adjustments immediately.

1. Not communicating with the crew or the team

I cannot overstate the importance of communication. A mic isn’t even necessary; I know it’s hard to type while you’re trying to pilot the ship, but you can get plans in order through team/crew chat before the game even begins. Of course, having a mic will make it possible to make on-the-fly changes to your basic strategy, which can oftentimes win you the game.

It does not matter how good individual crew members are at their jobs. No matter how good a gunner is, he will not be able to man every gun at once. No matter how good an engineer is, he will not be able to repair all the components at once. It is your job as captain to know and to communicate where your crew should divert their attention. Let gunners know which guns you want them to be using, and give them a good angle by moving your ship. Let engineers know if you want to retreat from an engagement, so they’ll know to ignore the guns and instead repair the engines, balloon, and hull.

Most people know to hit “X” for crew voice chat, but many seem unaware of the captains’ voice chat (hit “C”). This allows for communication between crews, albeit just between captains. This is vital for team coordination, especially on capture point maps. You can also use it to call for help, or to let another captain know to hold his ground and wait for you to back them up.

2. Bigger is better

It is tempting to take the helm of the Spire or the Galleon, with their imposing figures and numerous gun emplacements. I will be bold and say that this is usually a mistake. Of the two, the Galleon is the more user-friendly with her more or less symmetrical setup and guns on three of her four sides, but she remains a challenging ship to set up and pilot. A smaller ship means a simpler setup, which means a simpler strategy and easier work for the crewmen. I have found great success with the reliable Goldfish, even with pick up crews, simply because of how easy it is for them to understand my game plan. The effect of shorter distances between repairable components also cannot be ignored.

3. Slapdash setup

Captains often seem unaware of the effects of different damage types on different parts of an enemy ship. Some throw strategic armament out the window and focus on a single gun type, possibly with a harpoon thrown in (this is a terrible idea, by the way). Read up on damage types here. Yes, it is complicated. No, it’s not necessarily intuitive. Yes, you do need to know this. The linked page also shows you the range for every gun available. I mention this because many captains suffer from…

4. Range blindness

A ship with longer range always has the edge against her opponent. She will be able to begin the engagement on her own terms, and to put damage on the enemy ship without risking damage herself. There are other factors involved, of course: if the enemy ship is very maneuverable, the long-armed ship will find herself hitting air rather than hull, until the enemy is upon her. If the enemy ship has thick armor, she will only whittle away at the hull before the enemy engineers undo her work immediately. But in general, a ship that can deal damage from far away is an annoying and elusive opponent. A competent gunner on a flak gun or mercury rifle (ideally with Lesmok rounds) will make life hell for an enemy captain. Have at least one long-ranged gun on your ship. Know which way it is pointing, and point it toward a faraway enemy. Again, communicate. Talk to your gunner and find the ideal placement of your ship for bombarding the enemy from afar. Skilful piloting will enable you to stay out of the range of the enemy’s guns while you pelt them with shells.

Inevitably, some enemy ships will get up close. Perhaps they were just faster than your ship. Perhaps your guns couldn’t penetrate their armor. Perhaps their captains laid an ambush from inside a cloud or behind some debris. In any case, you must have a plan to deal with an enemy ship in close proximity. Running away at this point is futile; you will likely be unable to outrun the enemy’s guns before your ship falls apart. There is a variety of short-range guns designed for disruption rather than destruction. The cannonade will deflate the enemy’s balloons (see damage types), forcing them to deal with their drop in altitude while you make your escape. The flamethrower will catch many of the enemy ship’s components on fire, disabling guns and adding another step to fully repairing their ship. If your ship is capable of quick bursts of damage, the flamethrower is recommended, as it will allow you to turn the tables on the up-close opponent.

I have yet to find a good use for the harpoon. It is as yet too unreliable and unpredictable for strategic use, at least by my reckoning. It is possibly only useful as part of a very specific ship setup and battle strategy.

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Remember that you are taking on a lot of responsibility as the captain of a ship. You are not simply getting from point A to point B. You are the eyes and ears of the ship. Find enemy ships, discern their weak points, and deploy the strategy best suited to exploiting those weak points. Listen to the captains’ chatter and bring your ship where it is most needed. And once again: communicate. Tell the crew your long-term and short-term plans. Outline potential scenarios and the corresponding responses before entering the fray (for example, moving an engineer onto a cannonade or flamethrower when the enemy is up close); if your crew sticks with you — and they will, if you follow the above advice — they will eventually be where they need to be before you even tell them. This is the end goal. You, your crew, and your ship must act as one.

Good luck.

P.S.: I have elected not to write on personal loadouts, because it is difficult to recommend any single loadout when each captain will have his own idea of how to use the various “powerups” available to the pilot. There are many combinations, and most deal with a single, often circumstantial strategy. Powerups can save your ship, but there’s no “best” loadout (at least, to my belief), just the loadout that happens to match your piloting style and the situation at hand. The only piece of equipment I can recommend without reservation is the spyglass. Spotting an enemy with the spyglass gives you a not inconsiderable bonus to damage, and aids your gunner in aiming. Most savvy crewmen will bring their own spyglasses (as they know that they will almost never find themselves on the helm, and thus have no use for any other piloting equipment), but there is no guarantee that they will be available to spot ships in the midst of battle, which is when spotting makes the most difference.